Mbm_grdplot, SEGY data, *.all files from submerged platforms

Mbm_grdplot: Added colortable 10, which runs from blue to red and can be used for
plots of seismic reflection or subbottom profiler data when the trace signals are
both positive or negative.

SEGY format data: Changed MB-System SEGY traceheader to include a sensordepthtime
float value in bytes 216-219. This will be used to hold the two-way traveltime in
seconds corresponding to the source depth assuming a 1500 m/sec water sound speed.
This value can be used as a trace start delay time in plotting to account for the
source location of subbottom profiler data collected from submerged platforms like
AUVs and ROVs. The MB-System programs mbsegygrid and mbm_grdplot use the source
depth value in meters, but some external packages need the delay time.

SEGY format data: MB-System now recognizes file suffixes *.sgy and *.SGY in addition
to *.segy *.SEGY *.seg and *.SEG

Mbsegyinfo: Fixed calculation and reporting of trace minimum and maximum values.

Mbextractsegy: Now allows output of subbottom analytic data as well as envelope data.
Use of the -S4 command will output three separate segy files, one with the envelope
function, one with the subbottom correlate, and one with the correlate conjugant
(i.e. the Hilbert transform of the correlate). The section plot script generated now
will create plots of all three trace types.

Mbpreprocess and mbprocess: Now support merging navigation and attitude from Schmidt
Ocean Institute RVDAS format ROV navigation.

Mbpreprocess and format MBF_EM710RAW (58): The command --kluge-auv-sentry-sensordepth
now works for format 58 files (3rd generation Kongsberg multibeam data in *.all files)
such that available sensordepth values are embedded in the output format MBF_EM710MBA
(59) files.

ChangeLog.md

@@ -23,6 +23,7 @@ or beta, are equally accessible as tarballs through the Github interface.
 ### MB-System Version 5.8 Releases and Release Notes:
 ---
 
+- Version 5.8.1beta08    March 10, 2024
 - Version 5.8.1beta07    February 24, 2024
 - Version 5.8.1beta04    February 16, 2024
 - Version 5.8.1beta03    February 8, 2024
@@ -32,6 +33,39 @@ or beta, are equally accessible as tarballs through the Github interface.
 
 ---
 
+#### 5.8.1beta08 (March 10, 2024)
+
+Mbm_grdplot: Added colortable 10, which runs from blue to red and can be used for
+plots of seismic reflection or subbottom profiler data when the trace signals are
+both positive or negative.
+
+SEGY format data: Changed MB-System SEGY traceheader to include a sensordepthtime 
+float value in bytes 216-219. This will be used to hold the two-way traveltime in
+seconds corresponding to the source depth assuming a 1500 m/sec water sound speed.
+This value can be used as a trace start delay time in plotting to account for the
+source location of subbottom profiler data collected from submerged platforms like
+AUVs and ROVs. The MB-System programs mbsegygrid and mbm_grdplot use the source 
+depth value in meters, but some external packages need the delay time.
+
+SEGY format data: MB-System now recognizes file suffixes *.sgy and *.SGY in addition
+to *.segy *.SEGY *.seg and *.SEG
+
+Mbsegyinfo: Fixed calculation and reporting of trace minimum and maximum values.
+
+Mbextractsegy: Now allows output of subbottom analytic data as well as envelope data.
+Use of the -S4 command will output three separate segy files, one with the envelope
+function, one with the subbottom correlate, and one with the correlate conjugant
+(i.e. the Hilbert transform of the correlate). The section plot script generated now
+will create plots of all three trace types.
+
+Mbpreprocess and mbprocess: Now support merging navigation and attitude from Schmidt
+Ocean Institute RVDAS format ROV navigation.
+
+Mbpreprocess and format MBF_EM710RAW (58): The command --kluge-auv-sentry-sensordepth 
+now works for format 58 files (3rd generation Kongsberg multibeam data in *.all files)
+such that available sensordepth values are embedded in the output format MBF_EM710MBA
+(59) files.
+
 #### 5.8.1beta07 (February 24, 2024)
 
 CMake build system: Fixed ability to set OTPS location in cmake build system.

src/macros/mbm_grdplot

@@ -235,6 +235,11 @@ $ncpt = 11;
   @cptbg9 = (255, 200, 160, 145, 130, 100, 107, 123, 140, 160, 230);
   @cptbb9 = (100,  75,  50,  45,  40,  30,  24,   7,   0,   0,   0);
 
+# color palette 10 - Seismic (blue to white to red)
+  @cptbr10 = (  0,  51, 102, 153, 204, 255, 255, 255, 255, 255, 255);
+  @cptbg10 = (  0,  51, 102, 153, 204, 255, 204, 153, 102,  51,   0);
+  @cptbb10 = (255, 255, 255, 255, 255, 255, 204, 153, 102,  51,   0);
+
 # Determine the GMT version
 $gmt_version = `gmt --version`;
 
@@ -826,7 +831,7 @@ if ($color_control)
     ($color_style, $color_palette, $ncolors)
       = $color_control =~  /(\S+)\/(\S+)\/(\S+)/;
     if ($color_palette < 1
-      || $color_palette > 9)
+      || $color_palette > 10)
       {
       $color_palette = 1;
       }
@@ -840,7 +845,7 @@ if ($color_control)
     ($color_style, $color_palette) = $color_control
       =~  /(\S+)\/(\S+)/;
     if ($color_palette < 1
-      || $color_palette > 9)
+      || $color_palette > 10)
       {
       $color_palette = 1;
       }
@@ -1716,7 +1721,7 @@ elsif ($color_mode)
 if ($color_mode)
   {
   # deal with single colormap (not sealevel)
-  if ($color_palette < 8)
+  if ($color_palette < 8 || $color_palette == 10)
     {
     # set selected color palette
     eval "\@cptbr = \@cptbr$color_palette;";

src/man/man1/mbextractsegy.1

@@ -1,4 +1,4 @@
-.TH mbextractsegy 1 "3 June 2013" "MB-System 5.0" "MB-System 5.0"
+.TH mbextractsegy 1 "10 March 2024" "MB-System 5.0" "MB-System 5.0"
 .SH NAME
 \fBmbextractsegy\fP \- extracts subbottom profiler, center beam reflection,
 or seismic reflection data from swath data supported by MB-System and
@@ -195,27 +195,32 @@ be the input swath filename with ".segy" appended.
 .B \-S
 \fIsampleformat\fP
 .br
-Sets the sample format desired for use in the output SEGY file. Options include:
+Sets the sample format desired for use in the output SEGY data, which in turn
+determines how many SEGY files are output. Each SEGY file will contain one
+trace per ping (or shot); outputting multiple traces per ping creates
+multiple SEGY files. The options for \fIsampleformat\fP include:
  	MB_SEGY_SAMPLEFORMAT_NONE           1
  	MB_SEGY_SAMPLEFORMAT_TRACE          2
  	MB_SEGY_SAMPLEFORMAT_ENVELOPE       3
  	MB_SEGY_SAMPLEFORMAT_ANALYTIC       4
 .br
-MB_SEGY_SAMPLEFORMAT_TRACE implies that the seismic trace is in the original,
-most raw form with both positive and negative values.
-MB_SEGY_SAMPLEFORMAT_ANALYTIC implies that the trace has been
-been transformed from the original time series to an analytic signal containing
-both real and imaginary parts. Both the real and imaginary signals
-are stored in the SEGY file. MB_SEGY_SAMPLEFORMAT_ENVELOPE implies that the
-analytic signal has been reduced back to a single real, positive-only envelope
-signal by taking the magnitude of the real and imaginary parts at every sample.
-It is important to note that this option only sets the desired sample format, and
-the program may find it necessary to store the data in an alternate form. For
-instance, if the user specifies MB_SEGY_SAMPLEFORMAT_TRACE or
-MB_SEGY_SAMPLEFORMAT_ANALYTIC but the swath file only contains envelope data,
-the data will be written in the envelope form. The default value of
-MB_SEGY_SAMPLEFORMAT_NONE allows the program to choose the most appropriate
-sample format.
+The input seismic traces may be in three forms. The most basic form is a single
+acoustic or seismic signal time series with positive and negative values.
+An analytic signal is complex with the real and imaginary parts represented by
+two traces with positive and negative values. An envelope signal is calculated 
+as the magnitude of an analytic signal and so forms a single positive-only trace.
+The \fIsampleformat\fP sets the form of the output trace stored in one or more
+output SEGY files. If the output sample format differs from the input, then
+\fBmbextractsegy\fP must make the implied transformation. The default value of
+MB_SEGY_SAMPLEFORMAT_NONE to output data in the existing form. In the case of an
+output MB_SEGY_SAMPLEFORMAT_TRACE, a single trace is output. If the input is an
+analytic time series, then the output will be a single trace comprised of the
+real part of the signal. In the case of MB_SEGY_SAMPLEFORMAT_ENVELOPE, if the
+input is an analytic time series, then the single trace output will be an
+envelope function calculated from the analytic time series. In the case of
+MB_SEGY_SAMPLEFORMAT_ANALYTIC, then there will be three traces (and three
+SEGY files) output, the real part of the analytic data, the imaginary part
+of the analytic data, and the envelope function calculated from the analytic data.
 .TP
 .B \-U
 \fIrangethreshold\fP

src/man/man1/mbm_grdplot.1

@@ -1,4 +1,4 @@
-.TH mbm_grdplot 1 "11 May 2021" "MB-System 5.0" "MB-System 5.0"
+.TH mbm_grdplot 1 "10 March 2024" "MB-System 5.0" "MB-System 5.0"
 .SH NAME
 \fBmbm_grdplot\fP \- Create an executable shellscript which will generate
 a GMT map of gridded data in a GMT grd file or image data in a georeferenced
@@ -1188,6 +1188,11 @@ color palette 9 \- Sealevel 2
   green: 255 200 160 145 130 100 107 123 140 160 230
   blue:  100  75  50  45  40  30  24   7   0   0   0
 
+color palette 10 \- Seismic (blue to white to red)
+  red:     0  51 102 153 204 255 255 255 255 255 255
+  green:   0  51 102 153 204 255 204 153 102  51   0
+  blue:  255 255 255 255 255 255 204 153 102  51   0
+
 The Haxby colors have been adapted from a palette
 developed by Dr. William Haxby of the Lamont-Doherty
 Earth Observatory; this palette is pleasing to the

src/mbio/mb_access.c

@@ -1920,7 +1920,7 @@ int mb_extract_segytraceheader(int verbose, void *mbio_ptr, void *store_ptr, int
     fprintf(stderr, "dbg2       dummy1:            %f\n", mb_segytraceheader_ptr->dummy1);
     fprintf(stderr, "dbg2       dummy2:            %f\n", mb_segytraceheader_ptr->dummy2);
     fprintf(stderr, "dbg2       dummy3:            %f\n", mb_segytraceheader_ptr->dummy3);
-    fprintf(stderr, "dbg2       dummy4:            %f\n", mb_segytraceheader_ptr->dummy4);
+    fprintf(stderr, "dbg2       sensordepthtime:   %f\n", mb_segytraceheader_ptr->sensordepthtime);
     fprintf(stderr, "dbg2       soundspeed:        %f\n", mb_segytraceheader_ptr->soundspeed);
     fprintf(stderr, "dbg2       distance:          %f\n", mb_segytraceheader_ptr->distance);
     fprintf(stderr, "dbg2       dummy7:            %f\n", mb_segytraceheader_ptr->roll);
@@ -2025,7 +2025,7 @@ int mb_extract_segy(int verbose, void *mbio_ptr, void *store_ptr, int *samplefor
     fprintf(stderr, "dbg2       dummy1:         %f\n", mb_segytraceheader_ptr->dummy1);
     fprintf(stderr, "dbg2       dummy2:         %f\n", mb_segytraceheader_ptr->dummy2);
     fprintf(stderr, "dbg2       dummy3:         %f\n", mb_segytraceheader_ptr->dummy3);
-    fprintf(stderr, "dbg2       dummy4:         %f\n", mb_segytraceheader_ptr->dummy4);
+    fprintf(stderr, "dbg2       sensordepthtime:%f\n", mb_segytraceheader_ptr->sensordepthtime);
     fprintf(stderr, "dbg2       soundspeed:     %f\n", mb_segytraceheader_ptr->soundspeed);
     fprintf(stderr, "dbg2       distance:       %f\n", mb_segytraceheader_ptr->distance);
     fprintf(stderr, "dbg2       dummy7:         %f\n", mb_segytraceheader_ptr->roll);
@@ -2114,7 +2114,7 @@ int mb_insert_segy(int verbose, void *mbio_ptr, void *store_ptr, int kind, void
     fprintf(stderr, "dbg2       dummy1:         %f\n", mb_segytraceheader_ptr->dummy1);
     fprintf(stderr, "dbg2       dummy2:         %f\n", mb_segytraceheader_ptr->dummy2);
     fprintf(stderr, "dbg2       dummy3:         %f\n", mb_segytraceheader_ptr->dummy3);
-    fprintf(stderr, "dbg2       dummy4:         %f\n", mb_segytraceheader_ptr->dummy4);
+    fprintf(stderr, "dbg2       sensordepthtime:%f\n", mb_segytraceheader_ptr->sensordepthtime);
     fprintf(stderr, "dbg2       soundspeed:     %f\n", mb_segytraceheader_ptr->soundspeed);
     fprintf(stderr, "dbg2       distance:       %f\n", mb_segytraceheader_ptr->distance);
     fprintf(stderr, "dbg2       roll:           %f\n", mb_segytraceheader_ptr->roll);

src/mbio/mb_define.h

@@ -37,8 +37,8 @@
 #include <stdint.h>
 
 /* Define version and date for this release */
-#define MB_VERSION "5.8.1beta07"
-#define MB_VERSION_DATE "24 February 2024"
+#define MB_VERSION "5.8.1beta08"
+#define MB_VERSION_DATE "10 March 2024"
 
 /* CMake supports current OS's and so there is only one form of RPC and XDR and no mb_config.h file */
 #ifdef CMAKE_BUILD_SYSTEM

src/mbio/mb_format.c

@@ -2169,7 +2169,8 @@ int mb_get_format(int verbose, char *filename, char *fileroot, int *format, int
       i = strlen(filename) - 4;
     else
       i = 0;
-    if ((suffix = strstr(&filename[i], ".seg")) != NULL || (suffix = strstr(&filename[i], ".SEG")) != NULL)
+    if ((suffix = strstr(&filename[i], ".seg")) != NULL || (suffix = strstr(&filename[i], ".SEG")) != NULL 
+        || (suffix = strstr(&filename[i], ".sgy")) != NULL || (suffix = strstr(&filename[i], ".SGY")) != NULL)
       suffix_len = 4;
     else
       suffix_len = 0;